RetrogeneDB ID: retro_ggor_2735

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:75030306..75030928(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSGGOG00000001902
• Aliases: None
• Description: None

Sequence

>retro_ggor_2735
TGGAAGGTACCACTGGCCAGGGAGGGCCAGAAGCTGTGTCTGCACCAGCGACACTACATCGACAAGCTGGTGGAGGACAC
GGAGCACTGGCCCAAAGAAAACCTGGAGATCATCTTCACACAGTCTGTGGAGACACTTGGAGTCCGGGGTGACCTGATCT
CAGTAAAGAAATCTGTGGATCGGAATCAACTCCTTTCTCAGAGACTGGCTGCATATGCATCACTTGAAAACAAGAAGCTG
TTTGAAGAGGAGAAATTGCTGAGACCAGGAGGAAAGTTAGAGAAGATCCAGACCAAGGCAGGTGAGGCAACAGTGACATT
TCTGAAAAGCTGTCACCTGGAGGTAGGGATGAAGAACAGTGTCAAACGGGAGCTGAACCCTGAAACAGTTGCCCGCCACT
TCTTCAAGAATCTTGGAGTTGTGGTCACCCCCCCATACATTAAAATTACCAGAAGAGCCCCTCACTCGGTGGGGCAAGTA
CTGGTGTGAGGTGACGGTAAATGAGCTTGGTACTGTGAGGGTGCCTATGTCTCTGGTAAACTTTGAGAGGCCCAAAATCA
AAAGATAGAAGTACTGGTTAGCCCAGCAAGCTGCCAAGGGCATGGCCCCACCAGCCCCTAGA

Alignment

ORF - retro_ggor_2735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 77.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WKVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGRNRLLPQGLA
          WKVPLA.EG.K..LH.RH...KLVEDT.H.PKENLE.I.TQSVE..GVRGDL.SVKKS..RN.LL.Q.LA
Retrocopy WKVPLAREGQKLCLHQRHYIDKLVEDTEHWPKENLEIIFTQSVETLGVRGDLISVKKSVDRNQLLSQRLA

Parental  VYASPENKKLFEEEKSLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNVKWELNPEIVARHFFKNLGV
          .YAS.ENKKLFEEEK.LR..GKLEKIQTKAGEATV.FLKSC.LEVGMKN.VK.ELNPE.VARHFFKNLGV
Retrocopy AYASLENKKLFEEEKLLRPGGKLEKIQTKAGEATVTFLKSCHLEVGMKNSVKRELNPETVARHFFKNLGV

Parental  VVA-PHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKAMAPTSPQ
          VV..PHTLKLPEEP.TRWG.YWCEVTVN.L.TVRVPMS.VNFE.PK.KR.KYWLAQQAAK.MAP..P.
Retrocopy VVT>PHTLKLPEEPLTRWGKYWCEVTVNELGTVRVPMSLVNFERPKIKR*KYWLAQQAAKGMAPPAPR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	45.27 RPM
SRP007412_cerebellum	0.00 RPM	28.88 RPM
SRP007412_heart	0.00 RPM	13.16 RPM
SRP007412_kidney	0.00 RPM	39.05 RPM
SRP007412_liver	0.00 RPM	27.83 RPM
SRP007412_testis	0.00 RPM	66.41 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2735 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4078
Pan troglodytes	retro_ptro_2765
Pongo abelii	retro_pabe_3347

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735 ,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,